tidied by sean :)
library(tidyverse)
library(ggpubr)
library(ggsci)
library(gt)
library(emmeans)
distance <- read_csv("data/Target cells R21 DISTANCE.csv") |>
janitor::clean_names(replace=janitor:::mu_to_u) |>
mutate(donor = factor(donor),
replicate = factor(replicate))This document serves to analyze the distance from Thati’s dataset.
We can look at this data a few different ways:
distance |>
ggplot(aes(x= group,
y= distance_to_annotation_with_epithelium_um,
color= target_cell)) +
geom_boxplot(outlier.shape = NA) +
geom_point(position = position_jitterdodge(), alpha = 0.2) +
theme_pubr() +
scale_color_lancet() +
facet_grid(tissue*layer~target_cell, scales = "free") +
rotate_x_text(90)
distance |>
ggplot(aes(x=interaction(group,target_cell),
y=distance_to_annotation_with_epithelium_um,
color=target_cell)) +
geom_boxplot(outlier.shape = NA) +
geom_point(position = position_jitterdodge())+
theme_pubr()+
scale_color_lancet()+
facet_grid(~tissue*layer, scales = "free")+
rotate_x_text(45)
distance |>
filter(target_cell=="CD4") |>
ggplot(aes(x=group,
y=distance_to_annotation_with_epithelium_um,
color= group))+
geom_boxplot(outlier.shape = NA)+
geom_point(position = position_jitterdodge(), alpha = 0.3) +
theme_pubr()+
labs(title = "CD4+ Cells Only") +
scale_color_npg()
distance |>
ggplot(aes(x=group,
y=(distance_to_annotation_with_epithelium_um+0.1),
color=group))+
geom_boxplot(outlier.shape = NA)+
geom_point(position = position_jitterdodge())+
theme_pubr()+
scale_color_npg()+
facet_grid(tissue~target_cell)+
scale_y_log10()+
rotate_x_text(45)
distance |>
ggplot(aes(x=group,
y=distance_to_annotation_with_epithelium_um+0.1,
color=group))+
geom_boxplot(outlier.shape = NA)+
geom_point(position = position_jitterdodge())+
theme_pubr()+
scale_color_npg()+
facet_grid(tissue~target_cell)+
scale_y_log10()+
rotate_x_text(45)
# why bother taking a mean here?
mean_dist <- distance |>
group_by(condition, group, layer, donor, tissue, target_cell) |>
summarize(mean_distance_to_annotation_with_epithelium_um = mean(distance_to_annotation_with_epithelium_um))
mean_dist |>
ggplot(aes(x=layer,
y=mean_distance_to_annotation_with_epithelium_um,
color= interaction(group,condition)))+
geom_boxplot(outlier.shape = NA)+
geom_point(position = position_jitterdodge())+
theme_pubr()+
scale_color_npg()+
facet_wrap(~target_cell, scales = "free")
mean_dist |>
ggplot(aes(x=layer,
y=mean_distance_to_annotation_with_epithelium_um+1,
color=group))+
geom_boxplot(outlier.shape = NA)+
geom_point(position = position_jitterdodge())+
theme_pubr()+
scale_color_npg()+
facet_grid(tissue*condition~target_cell)+
scale_y_log10()+
rotate_x_text(45)
mean_dist |>
ggplot(aes(x=group,
y=mean_distance_to_annotation_with_epithelium_um+1,
color=layer)) +
geom_boxplot(outlier.shape = NA) +
geom_point(position = position_jitterdodge()) +
theme_pubr()+
scale_color_jco()+
facet_grid(tissue*condition~target_cell)+
scale_y_log10()
we can also make models to investigate this data:
glans <- mean_dist |>
filter(tissue == 'Glans')
model_glans <- lme4::lmer(mean_distance_to_annotation_with_epithelium_um ~ condition*group*layer*target_cell+(1|donor),
data = glans)
summary(model_glans)Linear mixed model fit by REML ['lmerMod']
Formula: mean_distance_to_annotation_with_epithelium_um ~ condition *
group * layer * target_cell + (1 | donor)
Data: glans
REML criterion at convergence: 5730.9
Scaled residuals:
Min 1Q Median 3Q Max
-2.9514 -0.4030 0.0035 0.3994 7.9078
Random effects:
Groups Name Variance Std.Dev.
donor (Intercept) 2309 48.05
Residual 4413 66.43
Number of obs: 546, groups: donor, 39
Fixed effects:
Estimate
(Intercept) 123.297
conditionUncircumcised 141.945
groupNon infected 65.960
layerEpithelium -57.125
target_cellCD3 62.306
target_cellCD3+CCR10 19.173
target_cellCD4 38.195
target_cellCD4+CCR10 94.855
target_cellCD4+CD3 63.890
target_cellCD4+CD3+CCR10 39.901
conditionUncircumcised:groupNon infected -148.805
conditionUncircumcised:layerEpithelium -190.897
groupNon infected:layerEpithelium -41.876
conditionUncircumcised:target_cellCD3 -70.061
conditionUncircumcised:target_cellCD3+CCR10 -85.649
conditionUncircumcised:target_cellCD4 11.181
conditionUncircumcised:target_cellCD4+CCR10 -89.778
conditionUncircumcised:target_cellCD4+CD3 -11.632
conditionUncircumcised:target_cellCD4+CD3+CCR10 -102.556
groupNon infected:target_cellCD3 -104.067
groupNon infected:target_cellCD3+CCR10 -68.044
groupNon infected:target_cellCD4 -72.287
groupNon infected:target_cellCD4+CCR10 -121.251
groupNon infected:target_cellCD4+CD3 -77.197
groupNon infected:target_cellCD4+CD3+CCR10 -79.722
layerEpithelium:target_cellCD3 -28.406
layerEpithelium:target_cellCD3+CCR10 8.658
layerEpithelium:target_cellCD4 -9.968
layerEpithelium:target_cellCD4+CCR10 -97.563
layerEpithelium:target_cellCD4+CD3 -49.681
layerEpithelium:target_cellCD4+CD3+CCR10 -15.259
conditionUncircumcised:groupNon infected:layerEpithelium 201.761
conditionUncircumcised:groupNon infected:target_cellCD3 -51.337
conditionUncircumcised:groupNon infected:target_cellCD3+CCR10 96.144
conditionUncircumcised:groupNon infected:target_cellCD4 8.424
conditionUncircumcised:groupNon infected:target_cellCD4+CCR10 167.294
conditionUncircumcised:groupNon infected:target_cellCD4+CD3+CCR10 119.120
conditionUncircumcised:layerEpithelium:target_cellCD3 108.185
conditionUncircumcised:layerEpithelium:target_cellCD3+CCR10 154.365
conditionUncircumcised:layerEpithelium:target_cellCD4 19.328
conditionUncircumcised:layerEpithelium:target_cellCD4+CCR10 158.933
conditionUncircumcised:layerEpithelium:target_cellCD4+CD3 -152.079
conditionUncircumcised:layerEpithelium:target_cellCD4+CD3+CCR10 158.680
groupNon infected:layerEpithelium:target_cellCD3 149.559
groupNon infected:layerEpithelium:target_cellCD3+CCR10 54.193
groupNon infected:layerEpithelium:target_cellCD4 12.855
groupNon infected:layerEpithelium:target_cellCD4+CCR10 47.127
groupNon infected:layerEpithelium:target_cellCD4+CD3 56.979
groupNon infected:layerEpithelium:target_cellCD4+CD3+CCR10 58.460
conditionUncircumcised:groupNon infected:layerEpithelium:target_cellCD3+CCR10 -187.747
conditionUncircumcised:groupNon infected:layerEpithelium:target_cellCD4 -46.039
conditionUncircumcised:groupNon infected:layerEpithelium:target_cellCD4+CD3+CCR10 -203.010
Std. Error
(Intercept) 35.771
conditionUncircumcised 45.365
groupNon infected 42.711
layerEpithelium 41.507
target_cellCD3 40.375
target_cellCD3+CCR10 37.286
target_cellCD4 38.773
target_cellCD4+CCR10 48.086
target_cellCD4+CD3 40.193
target_cellCD4+CD3+CCR10 37.446
conditionUncircumcised:groupNon infected 55.364
conditionUncircumcised:layerEpithelium 59.428
groupNon infected:layerEpithelium 59.472
conditionUncircumcised:target_cellCD3 55.219
conditionUncircumcised:target_cellCD3+CCR10 47.908
conditionUncircumcised:target_cellCD4 50.784
conditionUncircumcised:target_cellCD4+CCR10 57.154
conditionUncircumcised:target_cellCD4+CD3 68.721
conditionUncircumcised:target_cellCD4+CD3+CCR10 48.033
groupNon infected:target_cellCD3 84.310
groupNon infected:target_cellCD3+CCR10 47.840
groupNon infected:target_cellCD4 49.079
groupNon infected:target_cellCD4+CCR10 57.409
groupNon infected:target_cellCD4+CD3 68.506
groupNon infected:target_cellCD4+CD3+CCR10 47.988
layerEpithelium:target_cellCD3 53.136
layerEpithelium:target_cellCD3+CCR10 46.769
layerEpithelium:target_cellCD4 50.415
layerEpithelium:target_cellCD4+CCR10 87.463
layerEpithelium:target_cellCD4+CD3 55.594
layerEpithelium:target_cellCD4+CD3+CCR10 47.044
conditionUncircumcised:groupNon infected:layerEpithelium 83.734
conditionUncircumcised:groupNon infected:target_cellCD3 106.472
conditionUncircumcised:groupNon infected:target_cellCD3+CCR10 63.515
conditionUncircumcised:groupNon infected:target_cellCD4 65.787
conditionUncircumcised:groupNon infected:target_cellCD4+CCR10 72.447
conditionUncircumcised:groupNon infected:target_cellCD4+CD3+CCR10 63.626
conditionUncircumcised:layerEpithelium:target_cellCD3 78.279
conditionUncircumcised:layerEpithelium:target_cellCD3+CCR10 66.981
conditionUncircumcised:layerEpithelium:target_cellCD4 71.853
conditionUncircumcised:layerEpithelium:target_cellCD4+CCR10 101.601
conditionUncircumcised:layerEpithelium:target_cellCD4+CD3 116.820
conditionUncircumcised:layerEpithelium:target_cellCD4+CD3+CCR10 67.360
groupNon infected:layerEpithelium:target_cellCD3 97.340
groupNon infected:layerEpithelium:target_cellCD3+CCR10 66.828
groupNon infected:layerEpithelium:target_cellCD4 69.703
groupNon infected:layerEpithelium:target_cellCD4+CCR10 110.742
groupNon infected:layerEpithelium:target_cellCD4+CD3 96.500
groupNon infected:layerEpithelium:target_cellCD4+CD3+CCR10 67.174
conditionUncircumcised:groupNon infected:layerEpithelium:target_cellCD3+CCR10 94.775
conditionUncircumcised:groupNon infected:layerEpithelium:target_cellCD4 98.925
conditionUncircumcised:groupNon infected:layerEpithelium:target_cellCD4+CD3+CCR10 95.216
t value
(Intercept) 3.447
conditionUncircumcised 3.129
groupNon infected 1.544
layerEpithelium -1.376
target_cellCD3 1.543
target_cellCD3+CCR10 0.514
target_cellCD4 0.985
target_cellCD4+CCR10 1.973
target_cellCD4+CD3 1.590
target_cellCD4+CD3+CCR10 1.066
conditionUncircumcised:groupNon infected -2.688
conditionUncircumcised:layerEpithelium -3.212
groupNon infected:layerEpithelium -0.704
conditionUncircumcised:target_cellCD3 -1.269
conditionUncircumcised:target_cellCD3+CCR10 -1.788
conditionUncircumcised:target_cellCD4 0.220
conditionUncircumcised:target_cellCD4+CCR10 -1.571
conditionUncircumcised:target_cellCD4+CD3 -0.169
conditionUncircumcised:target_cellCD4+CD3+CCR10 -2.135
groupNon infected:target_cellCD3 -1.234
groupNon infected:target_cellCD3+CCR10 -1.422
groupNon infected:target_cellCD4 -1.473
groupNon infected:target_cellCD4+CCR10 -2.112
groupNon infected:target_cellCD4+CD3 -1.127
groupNon infected:target_cellCD4+CD3+CCR10 -1.661
layerEpithelium:target_cellCD3 -0.535
layerEpithelium:target_cellCD3+CCR10 0.185
layerEpithelium:target_cellCD4 -0.198
layerEpithelium:target_cellCD4+CCR10 -1.115
layerEpithelium:target_cellCD4+CD3 -0.894
layerEpithelium:target_cellCD4+CD3+CCR10 -0.324
conditionUncircumcised:groupNon infected:layerEpithelium 2.410
conditionUncircumcised:groupNon infected:target_cellCD3 -0.482
conditionUncircumcised:groupNon infected:target_cellCD3+CCR10 1.514
conditionUncircumcised:groupNon infected:target_cellCD4 0.128
conditionUncircumcised:groupNon infected:target_cellCD4+CCR10 2.309
conditionUncircumcised:groupNon infected:target_cellCD4+CD3+CCR10 1.872
conditionUncircumcised:layerEpithelium:target_cellCD3 1.382
conditionUncircumcised:layerEpithelium:target_cellCD3+CCR10 2.305
conditionUncircumcised:layerEpithelium:target_cellCD4 0.269
conditionUncircumcised:layerEpithelium:target_cellCD4+CCR10 1.564
conditionUncircumcised:layerEpithelium:target_cellCD4+CD3 -1.302
conditionUncircumcised:layerEpithelium:target_cellCD4+CD3+CCR10 2.356
groupNon infected:layerEpithelium:target_cellCD3 1.536
groupNon infected:layerEpithelium:target_cellCD3+CCR10 0.811
groupNon infected:layerEpithelium:target_cellCD4 0.184
groupNon infected:layerEpithelium:target_cellCD4+CCR10 0.426
groupNon infected:layerEpithelium:target_cellCD4+CD3 0.590
groupNon infected:layerEpithelium:target_cellCD4+CD3+CCR10 0.870
conditionUncircumcised:groupNon infected:layerEpithelium:target_cellCD3+CCR10 -1.981
conditionUncircumcised:groupNon infected:layerEpithelium:target_cellCD4 -0.465
conditionUncircumcised:groupNon infected:layerEpithelium:target_cellCD4+CD3+CCR10 -2.132
fit warnings:
fixed-effect model matrix is rank deficient so dropping 4 columns / coefficientsa <- pairs(lsmeans(model_glans, ~ layer))
b <- pairs(lsmeans(model_glans, ~ group))
c <- pairs(lsmeans(model_glans, ~ target_cell))
d <- pairs(lsmeans(model_glans, ~ condition))
b.a.c.d <- pairs(lsmeans(model_glans, ~ group | layer | target_cell |condition))
d.a.c.b <- pairs(lsmeans(model_glans, ~ condition| layer | target_cell | group))
c.d.b.a <- pairs(lsmeans(model_glans, ~ target_cell | condition | group | layer ))
GlansBigModel<-rbind(a,b,c, b.a.c.d,d.a.c.b,adjust="fdr")
table <- GlansBigModel |>
data.frame(stringsAsFactors = FALSE) |>
mutate(p.value = round(p.value, 5)) |>
mutate_at(c('estimate', 'SE', 'df', 't.ratio'), function(x){round(x, 2)}) |>
rename(`p value` = p.value, `t-ratio` = t.ratio, `d.f.` = df) |>
gt() |>
cols_align('center') |>
tab_source_note(
source_note = "P value adjustment: FDR"
) |>
tab_style(
style = cell_text(weight = "bold"),
locations = cells_body(
rows = `p value` < 0.05)
) |>
tab_header(
title = md("**GlansBigModel**")
) |>
gt:::as.tags.gt_tbl()
table| GlansBigModel | |||||||||
| layer | target_cell | condition | group | contrast | estimate | SE | d.f. | t-ratio | p value |
|---|---|---|---|---|---|---|---|---|---|
| . | . | . | . | Connective - Epithelium | NA | NA | NA | NA | NA |
| . | . | . | . | 4h - Non infected | NA | NA | NA | NA | NA |
| . | . | . | . | CCR10 - CD3 | NA | NA | NA | NA | NA |
| . | . | . | . | CCR10 - (CD3+CCR10) | 0.64 | 11.94 | 462.67 | 0.05 | 0.97553 |
| . | . | . | . | CCR10 - CD4 | -7.05 | 12.51 | 463.56 | -0.56 | 0.91842 |
| . | . | . | . | CCR10 - (CD4+CCR10) | NA | NA | NA | NA | NA |
| . | . | . | . | CCR10 - (CD4+CD3) | NA | NA | NA | NA | NA |
| . | . | . | . | CCR10 - (CD4+CD3+CCR10) | 0.18 | 12.02 | 462.86 | 0.01 | 0.98815 |
| . | . | . | . | CD3 - (CD3+CCR10) | NA | NA | NA | NA | NA |
| . | . | . | . | CD3 - CD4 | NA | NA | NA | NA | NA |
| . | . | . | . | CD3 - (CD4+CCR10) | NA | NA | NA | NA | NA |
| . | . | . | . | CD3 - (CD4+CD3) | NA | NA | NA | NA | NA |
| . | . | . | . | CD3 - (CD4+CD3+CCR10) | NA | NA | NA | NA | NA |
| . | . | . | . | (CD3+CCR10) - CD4 | -7.69 | 8.66 | 459.77 | -0.89 | 0.84355 |
| . | . | . | . | (CD3+CCR10) - (CD4+CCR10) | NA | NA | NA | NA | NA |
| . | . | . | . | (CD3+CCR10) - (CD4+CD3) | NA | NA | NA | NA | NA |
| . | . | . | . | (CD3+CCR10) - (CD4+CD3+CCR10) | -0.46 | 7.96 | 457.78 | -0.06 | 0.97553 |
| . | . | . | . | CD4 - (CD4+CCR10) | NA | NA | NA | NA | NA |
| . | . | . | . | CD4 - (CD4+CD3) | NA | NA | NA | NA | NA |
| . | . | . | . | CD4 - (CD4+CD3+CCR10) | 7.23 | 8.74 | 458.99 | 0.83 | 0.84823 |
| . | . | . | . | (CD4+CCR10) - (CD4+CD3) | NA | NA | NA | NA | NA |
| . | . | . | . | (CD4+CCR10) - (CD4+CD3+CCR10) | NA | NA | NA | NA | NA |
| . | . | . | . | (CD4+CD3) - (CD4+CD3+CCR10) | NA | NA | NA | NA | NA |
| Connective | CCR10 | Circumcised | . | 4h - Non infected | -65.96 | 42.73 | 463.40 | -1.54 | 0.50733 |
| Epithelium | CCR10 | Circumcised | . | 4h - Non infected | -24.08 | 41.40 | 461.88 | -0.58 | 0.91842 |
| Connective | CD3 | Circumcised | . | 4h - Non infected | 38.11 | 71.69 | 463.32 | 0.53 | 0.91842 |
| Epithelium | CD3 | Circumcised | . | 4h - Non infected | NA | NA | NA | NA | NA |
| Connective | CD3+CCR10 | Circumcised | . | 4h - Non infected | 2.08 | 21.55 | 457.12 | 0.10 | 0.97553 |
| Epithelium | CD3+CCR10 | Circumcised | . | 4h - Non infected | -10.23 | 21.55 | 457.12 | -0.47 | 0.93785 |
| Connective | CD4 | Circumcised | . | 4h - Non infected | 6.33 | 24.06 | 458.71 | 0.26 | 0.97553 |
| Epithelium | CD4 | Circumcised | . | 4h - Non infected | 35.35 | 28.01 | 460.12 | 1.26 | 0.56038 |
| Connective | CD4+CCR10 | Circumcised | . | 4h - Non infected | 55.29 | 38.59 | 460.82 | 1.43 | 0.51500 |
| Epithelium | CD4+CCR10 | Circumcised | . | 4h - Non infected | 50.04 | 83.75 | 463.51 | 0.60 | 0.91842 |
| Connective | CD4+CD3 | Circumcised | . | 4h - Non infected | 11.24 | 52.83 | 463.44 | 0.21 | 0.97553 |
| Epithelium | CD4+CD3 | Circumcised | . | 4h - Non infected | -3.87 | 56.83 | 462.43 | -0.07 | 0.97553 |
| Connective | CD4+CD3+CCR10 | Circumcised | . | 4h - Non infected | 13.76 | 21.88 | 457.53 | 0.63 | 0.91842 |
| Epithelium | CD4+CD3+CCR10 | Circumcised | . | 4h - Non infected | -2.82 | 22.53 | 458.00 | -0.13 | 0.97553 |
| Connective | CCR10 | Uncircumcised | . | 4h - Non infected | 82.85 | 35.25 | 465.86 | 2.35 | 0.17248 |
| Epithelium | CCR10 | Uncircumcised | . | 4h - Non infected | -77.04 | 47.67 | 460.47 | -1.62 | 0.48031 |
| Connective | CD3 | Uncircumcised | . | 4h - Non infected | 238.25 | 54.96 | 459.88 | 4.33 | 0.00032 |
| Epithelium | CD3 | Uncircumcised | . | 4h - Non infected | -71.20 | 55.46 | 462.68 | -1.28 | 0.56038 |
| Connective | CD3+CCR10 | Uncircumcised | . | 4h - Non infected | 54.74 | 23.10 | 463.50 | 2.37 | 0.17248 |
| Epithelium | CD3+CCR10 | Uncircumcised | . | 4h - Non infected | 28.41 | 23.10 | 463.50 | 1.23 | 0.56414 |
| Connective | CD4 | Uncircumcised | . | 4h - Non infected | 146.71 | 26.41 | 462.56 | 5.56 | 0.00000 |
| Epithelium | CD4 | Uncircumcised | . | 4h - Non infected | 20.01 | 27.77 | 463.84 | 0.72 | 0.90944 |
| Connective | CD4+CCR10 | Uncircumcised | . | 4h - Non infected | 36.80 | 27.61 | 464.51 | 1.33 | 0.56038 |
| Epithelium | CD4+CCR10 | Uncircumcised | . | 4h - Non infected | NA | NA | NA | NA | NA |
| Connective | CD4+CD3 | Uncircumcised | . | 4h - Non infected | NA | NA | NA | NA | NA |
| Epithelium | CD4+CD3 | Uncircumcised | . | 4h - Non infected | NA | NA | NA | NA | NA |
| Connective | CD4+CD3+CCR10 | Uncircumcised | . | 4h - Non infected | 43.45 | 23.10 | 463.50 | 1.88 | 0.29899 |
| Epithelium | CD4+CD3+CCR10 | Uncircumcised | . | 4h - Non infected | 28.11 | 24.01 | 459.53 | 1.17 | 0.59446 |
| Connective | CCR10 | . | 4h | Circumcised - Uncircumcised | -141.94 | 45.38 | 465.37 | -3.13 | 0.02527 |
| Epithelium | CCR10 | . | 4h | Circumcised - Uncircumcised | 48.95 | 44.40 | 461.11 | 1.10 | 0.63592 |
| Connective | CD3 | . | 4h | Circumcised - Uncircumcised | -71.88 | 38.25 | 411.65 | -1.88 | 0.29899 |
| Epithelium | CD3 | . | 4h | Circumcised - Uncircumcised | 10.83 | 40.86 | 435.71 | 0.27 | 0.97553 |
| Connective | CD3+CCR10 | . | 4h | Circumcised - Uncircumcised | -56.30 | 26.78 | 208.49 | -2.10 | 0.24810 |
| Epithelium | CD3+CCR10 | . | 4h | Circumcised - Uncircumcised | -19.76 | 26.78 | 208.49 | -0.74 | 0.90944 |
| Connective | CD4 | . | 4h | Circumcised - Uncircumcised | -153.13 | 31.62 | 309.39 | -4.84 | 0.00005 |
| Epithelium | CD4 | . | 4h | Circumcised - Uncircumcised | 18.44 | 34.07 | 353.37 | 0.54 | 0.91842 |
| Connective | CD4+CCR10 | . | 4h | Circumcised - Uncircumcised | -52.17 | 41.19 | 440.00 | -1.27 | 0.56038 |
| Epithelium | CD4+CCR10 | . | 4h | Circumcised - Uncircumcised | -20.20 | 73.99 | 491.73 | -0.27 | 0.97553 |
| Connective | CD4+CD3 | . | 4h | Circumcised - Uncircumcised | NA | NA | NA | NA | NA |
| Epithelium | CD4+CD3 | . | 4h | Circumcised - Uncircumcised | NA | NA | NA | NA | NA |
| Connective | CD4+CD3+CCR10 | . | 4h | Circumcised - Uncircumcised | -39.39 | 27.04 | 214.08 | -1.46 | 0.51500 |
| Epithelium | CD4+CD3+CCR10 | . | 4h | Circumcised - Uncircumcised | -7.17 | 27.67 | 226.97 | -0.26 | 0.97553 |
| Connective | CCR10 | . | Non infected | Circumcised - Uncircumcised | 6.86 | 38.35 | 411.97 | 0.18 | 0.97553 |
| Epithelium | CCR10 | . | Non infected | Circumcised - Uncircumcised | -4.00 | 50.64 | 483.16 | -0.08 | 0.97553 |
| Connective | CD3 | . | Non infected | Circumcised - Uncircumcised | 128.26 | 84.90 | 487.40 | 1.51 | 0.50733 |
| Epithelium | CD3 | . | Non infected | Circumcised - Uncircumcised | NA | NA | NA | NA | NA |
| Connective | CD3+CCR10 | . | Non infected | Circumcised - Uncircumcised | -3.63 | 27.43 | 221.39 | -0.13 | 0.97553 |
| Epithelium | CD3+CCR10 | . | Non infected | Circumcised - Uncircumcised | 18.88 | 27.43 | 221.39 | 0.69 | 0.91582 |
| Connective | CD4 | . | Non infected | Circumcised - Uncircumcised | -12.74 | 27.43 | 221.39 | -0.46 | 0.93785 |
| Epithelium | CD4 | . | Non infected | Circumcised - Uncircumcised | 3.10 | 29.44 | 264.69 | 0.11 | 0.97553 |
| Connective | CD4+CCR10 | . | Non infected | Circumcised - Uncircumcised | -70.66 | 32.32 | 321.57 | -2.19 | 0.22795 |
| Epithelium | CD4+CCR10 | . | Non infected | Circumcised - Uncircumcised | NA | NA | NA | NA | NA |
| Connective | CD4+CD3 | . | Non infected | Circumcised - Uncircumcised | 18.49 | 61.08 | 493.77 | 0.30 | 0.97553 |
| Epithelium | CD4+CD3 | . | Non infected | Circumcised - Uncircumcised | 159.71 | 84.91 | 487.44 | 1.88 | 0.29899 |
| Connective | CD4+CD3+CCR10 | . | Non infected | Circumcised - Uncircumcised | -9.70 | 27.43 | 221.39 | -0.35 | 0.97553 |
| Epithelium | CD4+CD3+CCR10 | . | Non infected | Circumcised - Uncircumcised | 23.76 | 28.30 | 240.49 | 0.84 | 0.84823 |
| P value adjustment: FDR | |||||||||
#htmltools::html_print(table)
#write.csv(GlansBigModel,"GlansBigModel.csv",row.names = F,quote = F)here we can see significant differences between CD3 and CD4 single positive cells in uncircumsized epithelium between infected and non infected– a significant difference was not detected in corresponding circumsized tissue:
distance |>
filter(layer == 'Connective' & (target_cell == 'CD4' | target_cell == 'CD3') & tissue == 'Glans') |>
ggplot(aes(x = group,
y = distance_to_annotation_with_epithelium_um,
color = group)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(alpha = 0.4) +
scale_y_log10() +
stat_compare_means(
comparisons = list(c('4h', 'Non infected')),
method = "wilcox.test",
label = "p.signif") +
facet_grid(rows = vars(target_cell), cols = vars(condition), scales = 'free') +
labs(title = "[not mean] CD4 Single Positive cells in Connective Tissue (Glans)") +
theme_pubr() + scale_color_lancet() 
mean_dist |>
filter(layer == 'Connective' & (target_cell == 'CD4' | target_cell == 'CD3') & tissue == 'Glans') |>
ggplot(aes(x = group,
y = mean_distance_to_annotation_with_epithelium_um,
color = group)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(alpha = 0.4) +
scale_y_log10() +
stat_compare_means(
comparisons = list(c('4h', 'Non infected')),
method = "wilcox.test",
label = "p.signif") +
facet_grid(rows = vars(target_cell), cols = vars(condition), scales = 'free') +
labs(title = "[mean] CD4 Single Positive cells in Connective Tissue (Glans)") +
theme_pubr() + scale_color_lancet() 
mean_dist |>
filter(layer == 'Epithelium' & target_cell == 'CD4' & group == '4h') |>
ggplot(aes(x = condition,
y = mean_distance_to_annotation_with_epithelium_um,
color = condition)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter() +
scale_y_log10() +
theme_pubr() + scale_color_lancet() 
#Check other combinations
pairs(lsmeans(model_glans, ~ condition| group | target_cell), adjust="fdr")group = 4h, target_cell = CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -46.50 33.6 344 -1.382 0.1679
group = Non infected, target_cell = CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 1.43 33.6 344 0.042 0.9661
group = 4h, target_cell = CD3:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -30.53 30.2 277 -1.011 0.3128
group = Non infected, target_cell = CD3:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised nonEst NA NA NA NA
group = 4h, target_cell = CD3+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -38.03 21.9 108 -1.738 0.0850
group = Non infected, target_cell = CD3+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 7.62 22.3 114 0.342 0.7333
group = 4h, target_cell = CD4:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -67.34 25.8 183 -2.613 0.0097
group = Non infected, target_cell = CD4:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -4.82 23.0 126 -0.210 0.8340
group = 4h, target_cell = CD4+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -36.18 43.7 457 -0.829 0.4077
group = Non infected, target_cell = CD4+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised nonEst NA NA NA NA
group = 4h, target_cell = CD4+CD3:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised nonEst NA NA NA NA
group = Non infected, target_cell = CD4+CD3:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 89.10 54.3 488 1.641 0.1014
group = 4h, target_cell = CD4+CD3+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -23.28 22.2 114 -1.047 0.2974
group = Non infected, target_cell = CD4+CD3+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 7.03 22.6 119 0.311 0.7562
Results are averaged over the levels of: layer
Degrees-of-freedom method: kenward-roger pairs(lsmeans(model_glans, ~ condition | group), adjust="fdr")group = 4h:
contrast estimate SE df z.ratio p.value
Circumcised - Uncircumcised nonEst NA NA NA NA
group = Non infected:
contrast estimate SE df z.ratio p.value
Circumcised - Uncircumcised nonEst NA NA NA NA
Results are averaged over the levels of: layer, target_cell
Degrees-of-freedom method: kenward-roger shaft <- mean_dist |>
filter(tissue == 'Shaft')
model_shaft <- lme4::lmer(mean_distance_to_annotation_with_epithelium_um ~ condition*group*layer*target_cell+(1|donor), data = shaft)
e <- pairs(lsmeans(model_shaft, ~ layer))
f <- pairs(lsmeans(model_shaft, ~ group))
g <- pairs(lsmeans(model_shaft, ~ target_cell))
h <- pairs(lsmeans(model_shaft, ~ condition))
f.e.g.h <- pairs(lsmeans(model_shaft, ~ group | layer | target_cell |condition))
e.g.h.f <- pairs(lsmeans(model_shaft, ~ condition| layer | target_cell | group))
ShaftBigModel<-rbind(e,f,g,f.e.g.h,e.g.h.f,adjust="fdr")
table <- ShaftBigModel |>
data.frame(stringsAsFactors = FALSE) |>
mutate(p.value = round(p.value, 5)) |>
mutate_at(c('estimate', 'SE', 'df', 't.ratio'), function(x){round(x, 2)}) |>
rename(`p value` = p.value, `t-ratio` = t.ratio, `d.f.` = df) |>
gt() |>
cols_align('center') |>
tab_source_note(
source_note = "P value adjustment: FDR"
) |>
tab_style(
style = cell_text(weight = "bold"),
locations = cells_body(
rows = `p value` < 0.05)
) |>
tab_header(
title = md("**ShaftBigModel**")
) |>
gt:::as.tags.gt_tbl()
#htmltools::html_print(table)
#write.csv(ShaftBigModel,"ShaftBigModel.csv",row.names = F,quote = F)
#Check other combinations
pairs(lsmeans(model_shaft, ~ condition| group | layer | target_cell),adjust="fdr")group = 4h, layer = Connective, target_cell = CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -21.0713 28.5 573 -0.738 0.4608
group = Non infected, layer = Connective, target_cell = CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 10.1754 20.6 455 0.493 0.6220
group = 4h, layer = Epithelium, target_cell = CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 3.0571 26.4 557 0.116 0.9080
group = Non infected, layer = Epithelium, target_cell = CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 18.6888 27.7 567 0.675 0.5002
group = 4h, layer = Connective, target_cell = CD3:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 47.8704 25.7 550 1.861 0.0633
group = Non infected, layer = Connective, target_cell = CD3:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -22.5521 35.5 589 -0.635 0.5256
group = 4h, layer = Epithelium, target_cell = CD3:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 23.9849 50.1 583 0.479 0.6323
group = Non infected, layer = Epithelium, target_cell = CD3:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised nonEst NA NA NA NA
group = 4h, layer = Connective, target_cell = CD3+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -15.0966 16.6 309 -0.907 0.3649
group = Non infected, layer = Connective, target_cell = CD3+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 14.8795 16.9 322 0.878 0.3805
group = 4h, layer = Epithelium, target_cell = CD3+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -2.1620 16.8 317 -0.129 0.8978
group = Non infected, layer = Epithelium, target_cell = CD3+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 13.9437 17.2 335 0.808 0.4194
group = 4h, layer = Connective, target_cell = CD4:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 20.0521 16.8 317 1.192 0.2341
group = Non infected, layer = Connective, target_cell = CD4:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 16.3006 17.1 328 0.954 0.3409
group = 4h, layer = Epithelium, target_cell = CD4:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -5.3991 20.6 455 -0.262 0.7936
group = Non infected, layer = Epithelium, target_cell = CD4:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 4.7744 17.3 339 0.275 0.7832
group = 4h, layer = Connective, target_cell = CD4+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -16.3627 18.1 370 -0.905 0.3662
group = Non infected, layer = Connective, target_cell = CD4+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 26.2832 17.8 357 1.478 0.1402
group = 4h, layer = Epithelium, target_cell = CD4+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -4.8517 20.9 462 -0.233 0.8162
group = Non infected, layer = Epithelium, target_cell = CD4+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 71.9048 28.5 573 2.520 0.0120
group = 4h, layer = Connective, target_cell = CD4+CD3:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 19.7154 23.7 523 0.832 0.4059
group = Non infected, layer = Connective, target_cell = CD4+CD3:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 31.5623 35.5 590 0.890 0.3737
group = 4h, layer = Epithelium, target_cell = CD4+CD3:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 0.0892 33.0 587 0.003 0.9978
group = Non infected, layer = Epithelium, target_cell = CD4+CD3:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -2.2759 35.5 589 -0.064 0.9489
group = 4h, layer = Connective, target_cell = CD4+CD3+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 1.3707 16.6 309 0.082 0.9344
group = Non infected, layer = Connective, target_cell = CD4+CD3+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 13.2897 16.9 322 0.784 0.4334
group = 4h, layer = Epithelium, target_cell = CD4+CD3+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -0.6495 17.7 352 -0.037 0.9707
group = Non infected, layer = Epithelium, target_cell = CD4+CD3+CCR10:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised -5.0843 17.5 345 -0.291 0.7715
Degrees-of-freedom method: kenward-roger pairs(lsmeans(model_shaft, ~ condition | group | layer),adjust="fdr")group = 4h, layer = Connective:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 5.21 11.3 87.3 0.462 0.6452
group = Non infected, layer = Connective:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 12.85 12.1 113.4 1.060 0.2914
group = 4h, layer = Epithelium:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised 2.01 13.4 161.7 0.150 0.8812
group = Non infected, layer = Epithelium:
contrast estimate SE df t.ratio p.value
Circumcised - Uncircumcised nonEst NA NA NA NA
Results are averaged over the levels of: target_cell
Degrees-of-freedom method: kenward-roger #Data_1_Dist_MeanTotals<-aggregate(Total.Cells/Area.mm.2~condition+group+Tissue+Donor+layer+target_ce#ll, data = Data_1_Dist,mean)